Commits for max

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

eb6a35ecac2424ecf5b2b874dff935353e4f0a53 Wed Dec 9 01:29:24 2020 -0800

• another super old trackDb docs mistake, no redmine
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 1, context: html, text, full: html, text

c8bef32e9a011410ae03ed0b44316085c8df86ff Thu Dec 10 01:58:41 2020 -0800

• add the fonts packages to gbic installer script, refs #25525
  • src/product/installer/browserSetup.sh - lines changed 2, context: html, text, full: html, text

4fcea62ede5b34df814333e242a865fb20dfb821 Thu Dec 10 02:57:37 2020 -0800

• adding linux commands to bigBed example 2, no redmine yet, but probably coming.
  • src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 19, context: html, text, full: html, text

54edad8bebf1ef9763b9f16ec2c34143c447aafa Thu Dec 10 06:17:14 2020 -0800

• auto-detecting track type bigInteract if custom track file ends with .inter.bb or .inter.bigBed, no redmine
  • src/hg/lib/customFactory.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/customTrack.c - lines changed 2, context: html, text, full: html, text

16a0bb49dfcbf27c039d99e4ab40a41c59814400 Fri Dec 11 05:56:03 2020 -0800

• a quickstart section for the bigBed.html page, may be not optimal yet, but to illustrate the idea more
  • src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 72, context: html, text, full: html, text

679e26dcf187dd96851052d91081abf9c6864d4b Mon Dec 14 05:44:14 2020 -0800

• small fixed to bigBed docs page, refs #26677
  • src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 19, context: html, text, full: html, text

231229599259249d0b0a00be9dd95b64d9d9a48c Tue Dec 15 01:58:10 2020 -0800

• adding VCF test case to chromToUcsc, no new feature or code change, so no redmine
  • src/utils/chromToUcsc/tests/expected/hg19.vcf - lines changed 500, context: html, text, full: html, text
  • src/utils/chromToUcsc/tests/in/hg19.vcf - lines changed 500, context: html, text, full: html, text
  • src/utils/chromToUcsc/tests/makefile - lines changed 1, context: html, text, full: html, text

cf1446a79ba6729f0d88f1ccca523d9604d758ca Tue Dec 15 02:09:54 2020 -0800

• fixing up the chromToUcsc test case to use a more realistic vcf.gz file, refs #26672
  • src/utils/chromToUcsc/chromToUcsc - lines changed 2, context: html, text, full: html, text
  • src/utils/chromToUcsc/tests/in/hg19.vcf - lines changed 500, context: html, text, full: html, text
  • src/utils/chromToUcsc/tests/in/hg19.vcf.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

572f8e2a5e67250ee2802f039a8b97d2322cc99a Tue Dec 15 02:16:25 2020 -0800

• documenting supported file formats, refs #26689
  • src/utils/chromToUcsc/chromToUcsc - lines changed 3, context: html, text, full: html, text

a115ebc88f157c14032c4bb63ca8f7b453998ce5 Tue Dec 15 03:40:00 2020 -0800

• UniProt track should not show title but label on mouseover rightclick, refs #26687
  • src/hg/js/hgTracks.js - lines changed 1, context: html, text, full: html, text

54197358a1407de6898c360a38df822257338112 Tue Dec 15 05:33:49 2020 -0800

• updating hgmd and ncbiRefseqHgmd to HGMD 2020, refs #24625
  • src/hg/makeDb/doc/hg19.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hgmd.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/ncbiRefSeq.txt - lines changed 2, context: html, text, full: html, text

02836b99a074f08b3be77de8933bf7fb5f0fe00c Wed Dec 16 06:26:34 2020 -0800

• show exon numbers configuration option was ignored for genePred and bigGenePred tracks, the exonNumbers cart variable now is taken into account refs #25325
  • src/hg/hgTracks/simpleTracks.c - lines changed 9, context: html, text, full: html, text

866a89e5704f4bde33de441b72016347a0cdd180 Tue Dec 22 06:01:02 2020 -0800

• adding hub.conf to Jim's new tool test directory
  • src/utils/clusterMatrixToBarChartBed/tests/hub.conf - lines changed 23, context: html, text, full: html, text